I purchased one of your (ESP8266-07 BREAKOUT AND POWER SUPPLY BOARD). I have re-flashed it on NodeMCU firmware binary to ESP8266. The Reflash NodeMCU firmware binary to ESP8266, work great. Now I am having trouble with Arduino IED, connecting to the new reflash esp8266.

I am using NodeMCU(esp8266-12E bored) and the right port. If you can give me some help I'd appreciate it thank you.

You need to choose a module with the same memory size as the one you have. The ESP8266-12E has a bigger flash memory than the ESP8266-07 that is on the breakout board you purchased. You have to choose 'Generic ESP8266 Module' from the Board Manager menu. Also, you have to press and release the Reset while holding down the Flash button before starting the download.